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Alpha 6.0: --r[2]-[un]phased
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@chrchang chrchang released this 11 Nov 21:06
· 7 commits to master since this release
v2.0.0-a.6.0
39d4f67

New features:

  • LD-matrix computation (--r[2]-unphased)
  • --glm qt-residualize mode
  • --hwe enhancements for biobank-scale data: support for p-values < 2.23e-308, and sample-size-based thresholds
  • --ref-allele/--alt1-allele/--ref-from-fa/--maj-ref support for multiallelic variants
  • --check-sex/--impute-sex

Other significant behavior changes relative to alpha 5:

  • --allow-extra-chr is never necessary any more
  • --set-all-var-ids and related flags are now applied to all --pmerge[-list] inputs
  • Polyploid genotypes in VCF/BCF files now default to triggering an error; this behavior is controlled by the --polyploid-mode flag
  • -log10(x) column names now consistently start with "NEG_LOG10_", instead of "LOG10_"
  • --adjust[-file] QQ column is no longer affected by the 'log10' modifier
  • Most computations now consider unknown-sex samples on chrY, unless they explicitly state otherwise
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